X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmol.java;h=bab8a2d7fc145b9a577425674a6d5f0c6933746b;hb=58afea88095280d807e5c2ac8b9155de5ba3503c;hp=cc37b66af6c036bde7b0264af97cf48b563b4fb3;hpb=cb5d856b1304448cae13a333cbd9017f81520d90;p=jalview.git
diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java
index cc37b66..bab8a2d 100644
--- a/src/jalview/gui/AppJmol.java
+++ b/src/jalview/gui/AppJmol.java
@@ -1,25 +1,28 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
* Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import java.util.*;
import java.awt.*;
+
import javax.swing.*;
import javax.swing.event.*;
@@ -28,17 +31,19 @@ import java.io.*;
import jalview.jbgui.GStructureViewer;
import jalview.api.SequenceStructureBinding;
+import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.datamodel.*;
import jalview.gui.ViewSelectionMenu.ViewSetProvider;
import jalview.datamodel.PDBEntry;
+import jalview.ext.jmol.JalviewJmolBinding;
import jalview.io.*;
import jalview.schemes.*;
import jalview.util.MessageManager;
import jalview.util.Platform;
public class AppJmol extends GStructureViewer implements Runnable,
- SequenceStructureBinding, ViewSetProvider
+ ViewSetProvider, JalviewStructureDisplayI
{
AppJmolBinding jmb;
@@ -172,7 +177,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
_alignwith = new Vector();
}
- seqColourBy = new ViewSelectionMenu("Colour by ..", this, _colourwith,
+ seqColourBy = new ViewSelectionMenu(MessageManager.getString("label.colour_by"), this, _colourwith,
new ItemListener()
{
@@ -192,7 +197,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
});
viewMenu.add(seqColourBy);
final ItemListener handler;
- JMenu alpanels = new ViewSelectionMenu("Superpose with ..", this,
+ JMenu alpanels = new ViewSelectionMenu(MessageManager.getString("label.superpose_with"), this,
_alignwith, handler = new ItemListener()
{
@@ -200,7 +205,11 @@ public class AppJmol extends GStructureViewer implements Runnable,
public void itemStateChanged(ItemEvent e)
{
alignStructs.setEnabled(_alignwith.size() > 0);
- alignStructs.setToolTipText(MessageManager.formatMessage("label.align_structures_using_linked_alignment_views", new String[] {new Integer(_alignwith.size()).toString()}));
+ alignStructs.setToolTipText(MessageManager
+ .formatMessage(
+ "label.align_structures_using_linked_alignment_views",
+ new String[]
+ { new Integer(_alignwith.size()).toString() }));
}
});
handler.itemStateChanged(null);
@@ -252,9 +261,11 @@ public class AppJmol extends GStructureViewer implements Runnable,
if (alreadyMapped != null)
{
int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- MessageManager.formatMessage("label.pdb_entry_is_already_displayed", new String[]{pdbentry.getId()}),
- MessageManager.formatMessage("label.map_sequences_to_visible_window", new String[]{pdbentry.getId()}),
- JOptionPane.YES_NO_OPTION);
+ MessageManager.formatMessage(
+ "label.pdb_entry_is_already_displayed", new String[]
+ { pdbentry.getId() }), MessageManager.formatMessage(
+ "label.map_sequences_to_visible_window", new String[]
+ { pdbentry.getId() }), JOptionPane.YES_NO_OPTION);
if (option == JOptionPane.YES_OPTION)
{
@@ -309,10 +320,15 @@ public class AppJmol extends GStructureViewer implements Runnable,
{
AppJmol topJmol = (AppJmol) jm.nextElement();
// TODO: highlight topJmol in view somehow
- int option = JOptionPane.showInternalConfirmDialog(Desktop.desktop,
- MessageManager.formatMessage("label.add_pdbentry_to_view", new String[]{pdbentry.getId(),topJmol.getTitle()}),
- MessageManager.getString("label.align_to_existing_structure_view"),
- JOptionPane.YES_NO_OPTION);
+ int option = JOptionPane
+ .showInternalConfirmDialog(
+ Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.add_pdbentry_to_view", new String[]
+ { pdbentry.getId(), topJmol.getTitle() }),
+ MessageManager
+ .getString("label.align_to_existing_structure_view"),
+ JOptionPane.YES_NO_OPTION);
if (option == JOptionPane.YES_OPTION)
{
topJmol.useAlignmentPanelForSuperposition(ap);
@@ -617,7 +633,8 @@ public class AppJmol extends GStructureViewer implements Runnable,
{
return;
}
- JMenuItem menuItem = new JMenuItem(MessageManager.getString("label.all"));
+ JMenuItem menuItem = new JMenuItem(
+ MessageManager.getString("label.all"));
menuItem.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent evt)
@@ -674,7 +691,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
jmb.centerViewer(toshow);
}
- void closeViewer()
+ public void closeViewer()
{
jmb.closeViewer();
ap = null;
@@ -779,9 +796,12 @@ public class AppJmol extends GStructureViewer implements Runnable,
if (errormsgs.length() > 0)
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.formatMessage("label.pdb_entries_couldnt_be_retrieved", new String[]{errormsgs.toString()}),
- MessageManager.getString("label.couldnt_load_file"), JOptionPane.ERROR_MESSAGE);
+ JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager
+ .formatMessage("label.pdb_entries_couldnt_be_retrieved",
+ new String[]
+ { errormsgs.toString() }), MessageManager
+ .getString("label.couldnt_load_file"),
+ JOptionPane.ERROR_MESSAGE);
}
long lastnotify = jmb.getLoadNotifiesHandled();
@@ -829,7 +849,8 @@ public class AppJmol extends GStructureViewer implements Runnable,
// need to wait around until script has finished
while (addingStructures ? lastnotify >= jmb.getLoadNotifiesHandled()
- : (jmb.isFinishedInit() && jmb.getPdbFile().length != jmb.pdbentry.length))
+ : (jmb.isFinishedInit() && jmb.getPdbFile() != null && jmb
+ .getPdbFile().length != jmb.pdbentry.length))
{
try
{
@@ -871,7 +892,7 @@ public class AppJmol extends GStructureViewer implements Runnable,
chooser.setFileView(new JalviewFileView());
chooser.setDialogTitle("Save PDB File");
- chooser.setToolTipText(MessageManager.getString("action.save"));
+ chooser.setToolTipText(MessageManager.getString("action.save"));
int value = chooser.showSaveDialog(this);
@@ -919,8 +940,9 @@ public class AppJmol extends GStructureViewer implements Runnable,
cap.dispose();
return;
}
- jalview.gui.Desktop.addInternalFrame(cap, MessageManager.getString("label.pdb_sequence_mapping"),
- 550, 600);
+ jalview.gui.Desktop.addInternalFrame(cap,
+ MessageManager.getString("label.pdb_sequence_mapping"), 550,
+ 600);
}
/**
@@ -1142,7 +1164,8 @@ public class AppJmol extends GStructureViewer implements Runnable,
g.fillRect(0, 0, currentSize.width, currentSize.height);
g.setColor(Color.white);
g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString(MessageManager.getString("label.error_loading_file") + "...", 20, currentSize.height / 2);
+ g.drawString(MessageManager.getString("label.error_loading_file")
+ + "...", 20, currentSize.height / 2);
StringBuffer sb = new StringBuffer();
int lines = 0;
for (int e = 0; e < jmb.pdbentry.length; e++)
@@ -1167,7 +1190,8 @@ public class AppJmol extends GStructureViewer implements Runnable,
g.fillRect(0, 0, currentSize.width, currentSize.height);
g.setColor(Color.white);
g.setFont(new Font("Verdana", Font.BOLD, 14));
- g.drawString(MessageManager.getString("label.retrieving_pdb_data"), 20, currentSize.height / 2);
+ g.drawString(MessageManager.getString("label.retrieving_pdb_data"),
+ 20, currentSize.height / 2);
}
else
{
@@ -1335,4 +1359,9 @@ public class AppJmol extends GStructureViewer implements Runnable,
return !jmb.isColourBySequence();
}
+ public JalviewJmolBinding getBinding()
+ {
+ return jmb;
+ }
+
}